Upwelling ecosystems are particularly heterogeneous and present intense meso- (tens of kilometers) and sub-mesoscale (hundreds of meters to kilometers) activity that are expected to drive the distribution of the organisms, and thus their interactions. Here we addressed the impact of the physical forcing in the northern Humboldt Current system off Peru, which is characterized by the presence of an intense and shallow oxygen minimum zone (OMZ), and used the variability of the depth of the oxycline as a proxy of the physical forcing which impacts the epipelagic communities. We analyzed simultaneous high-resolution acoustic observations of the oxycline depth, the biomass in macrozooplankton, and the biomass in pelagic fish. Three complementary methodologies were considered: (i) geostatistical methods and correlation tests, (ii) principal coordinates of neighbour matrices, and (iii) wavelet analysis. Our results highlight the relevance of a multi-method framework to characterize the multiscale relationships between marine ecosystem components. We also provided evidence that the submesoscale-to-mesoscale variability of the oxycline depth drives the distribution of macrozooplankton which further structures the distribution of forage fish in a bottom-up cascade.